The Abdo lab is interested in studying the microbiome, its interactions and function, and how it interacts with and affects its hosts’ health and is affected by its surrounding environment. This specifically includes studying the relationship between host immune system and the microbiome as it is influenced by external perturbations including vaccination, prebiotics, probiotics, antibiotics and other factors such as viral, or other, infections. This is in addition studying viral evolution and plasmid transfer and evolution as it impacts acquisition, transmission and maintenance of antimicrobial resistance. Another interest of the Abdo Lab is focused on developing and applying computational tools for processing and analysis of high throughput sequence data, and the associated metadata, in addition to developing inferential and predictive models and machine learning methods to facilitate understanding of these complex biological systems.
Some of the software generated through the Abdo lab is available on Github: https://github.com/Abdo-Lab.
The Abdo lab is part of the CSU Microbiome Network.
Mucosal Immunity and the Microbiome
Challenge: Little is known about changes in the gut microbiome during vaccination, especially with an oral-probiotic vector.
Objective: Evaluate use of Lactobacillus acidophilus as a probiotic vaccine vector and the reciprocal interactions between the host’s immune response and alterations in the gut microbiome.
Antimicrobial Resistance and the Microbiome
Challenge: Little is known about antimicrobial resistance reservoirs in natural environments, especially in food production. Hard to link mobile genetic elements to host microbes.
Objective: Examine the impact of both limiting and removing antibiotic use on the resistome and antimicrobial resistance evolution in poultry (food) production.
Viral Ecology and Evolution
Challenge: Whole Genome Sequencing of AIV provides a faster more accurate approach and removes need for propagation in chicken eggs for AIV diagnostics.
Objective: Evaluate impact of virus isolation on virus mutation, natural selection, reassortment, and detection of co-infections.
Methods for Metagenomics Classification and Modeling
Challenge: Large data sets are generated using high throughput sequencing and scalable computational tools to process and classify these data are lacking.
Objective: Develop a fast and accurate classification method for high throughput shotgun metagenomics data utilizing Low-Density Parity-Check and Naïve Bayes Classifier implemented using GPU computing.
Population genomic transformations induced by isolation of wild bird avian influenza viruses (Orthomyxoviridae) in embryonated chicken eggs
Hopken M, Piaggio A, Pabilonia K, Pierce J, Anderson T, Pierce C, Abdo Z. 2020.
Impact of oral probiotic Lactobacillus acidophilus vaccine strains on the immune response and gut microbiome of mice
Z Abdo, J LeCureux, A LaVoy, B Eklund, EP Ryan, GA Dean. 2019.
PloS one 14 (12), e0225842
Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis
N Noyes, KC Cho, J Ravel, LJ Forney, Z Abdo. 2018.
PLoS One 13 (1), e0191625
Fast maximum likelihood estimation and supervised classification for the Beta-Liouville Multinomial.
Lakin, S. M. and Z. Abdo. 2020.
Reads2Resistome: an adaptable and high-throughput whole-genome sequencing pipeline for bacterial resistome characterization.
Woyda, R., A. Oladeinde, Z. Abdo. 2020.
BioRxiv, doi: https://doi.org/10.1101/2020.05.18.102715
news and updates
A USDA-funded study finds that the microbiome in reused poultry litter can deter growth of pathogens like Salmonella.
Scientists across the university, in the CSU Microbiome Network, tackle important questions in the expanding field of microbiome research.
Graduate student Bridget Eklund, mentored by Drs. Zaid Abdo and Gregg Dean, placed first in the Basic Oral Presentations category of the annual CVMBS Research Day.
Lab: Research Innovation Center (RIC) room D139
Office: Research Innovation Center (RIC) room D114